propka.parameters

Configuration file parameters

Holds parameters and settings that can be set in propka.cfg. The file format consists of lines of keyword value [value ...], blank lines, and comment lines (introduced with #).

The module attributes below list the names and types of all key words in configuration file.

Classes

InteractionMatrix(name)	Interaction matrix class.
PairwiseMatrix(name)	Pairwise interaction matrix class.
Parameters(interaction_matrix, ...)	PROPKA parameter class.
squared_property()

class propka.parameters.InteractionMatrix(name: str)

Interaction matrix class.

add(words: Sequence[str])

Add values to matrix.

Parameters:

words – values to add

get_value(item1: str, item2: str) → str | float | None

Get specific matrix value.

Parameters:

• item1 – matrix row index

• item2 – matrix column index

Returns:

matrix value or None

keys()

Get keys from matrix.

Returns:

dictionary key list

class propka.parameters.PairwiseMatrix(name: str)

Pairwise interaction matrix class.

add(words: Sequence[str])

Add information to the matrix.

TODO - this function unnecessarily bundles arguments into a tuple

Parameters:

words – tuple with assignment information and value

get_value(item1: str, item2: str) → Tuple[float, float]

Get specified value from matrix.

Parameters:

• item1 – row index

• item2 – column index

Returns:

matrix value (or default)

insert(key1: str, key2: str, value: Tuple[float, float])

Insert value into matrix.

Parameters:

• key1 – first matrix key (row)

• key2 – second matrix key (column)

• value – value to insert

keys()

Get keys from matrix.

Returns:

dictionary key list

class propka.parameters.Parameters(interaction_matrix: ~propka.parameters.InteractionMatrix = <factory>, sidechain_cutoffs: ~propka.parameters.PairwiseMatrix = <factory>, VanDerWaalsVolume: ~typing.Dict[str, float] = <factory>, charge: ~typing.Dict[str, float] = <factory>, model_pkas: ~typing.Dict[str, float] = <factory>, ions: ~typing.Dict[str, float] = <factory>, valence_electrons: ~typing.Dict[str, float] = <factory>, custom_model_pkas: ~typing.Dict[str, float] = <factory>, backbone_NH_hydrogen_bond: ~typing.Dict[str, list] = <factory>, backbone_CO_hydrogen_bond: ~typing.Dict[str, list] = <factory>, protein_group_mapping: ~typing.Dict[str, str] = <factory>, ignore_residues: ~typing.List[str] = <factory>, angular_dependent_sidechain_interactions: ~typing.List[str] = <factory>, acid_list: ~typing.List[str] = <factory>, base_list: ~typing.List[str] = <factory>, exclude_sidechain_interactions: ~typing.List[str] = <factory>, backbone_reorganisation_list: ~typing.List[str] = <factory>, write_out_order: ~typing.List[str] = <factory>, desolv_cutoff: float = 20.0, buried_cutoff: float = 15.0, coulomb_cutoff1: float = 4.0, coulomb_cutoff2: float = 10.0, version: str = 'VersionA', output_file_tag: str = '', ligand_typing: str = 'groups', pH: str = 'variable', reference: str = 'neutral', Nmin: int = 280, Nmax: int = 560, desolvationSurfaceScalingFactor: float = 0.25, desolvationPrefactor: float = -13.0, desolvationAllowance: float = 0.0, coulomb_diel: float = 80.0, COO_HIS_exception: float = 1.6, OCO_HIS_exception: float = 1.6, CYS_HIS_exception: float = 1.6, CYS_CYS_exception: float = 3.6, min_ligand_model_pka: float = -10.0, max_ligand_model_pka: float = 20.0, coupling_max_number_of_bonds: int = 3, min_bond_distance_for_hydrogen_bonds: int = 4, shared_determinants: bool = False, common_charge_centre: bool = False, remove_penalised_group: bool = True, max_intrinsic_pka_diff: float = 2.0, min_interaction_energy: float = 0.5, max_free_energy_diff: float = 1.0, min_swap_pka_shift: float = 1.0, min_pka: float = 0.0, max_pka: float = 10.0, sidechain_interaction: float = 0.85)

PROPKA parameter class.

parse_line(line)

Parse parameter file line.

parse_parameter(words, typefunc: Callable[[str], T])

Parse field to parameters.

Parameters:

words – strings to parse

parse_string(words)

Parse field to strings.

Parameters:

words – strings to parse

parse_to_list_dictionary(words: List[str])

Parse field to list dictionary.

Parameters:

words – strings to parse.

parse_to_matrix(words)

Parse field to matrix.

Parameters:

words – strings to parse

parse_to_number_dictionary(words)

Parse field to number dictionary.

Parameters:

words – strings to parse.

parse_to_string_dictionary(words)

Parse field to string dictionary.

Parameters:

words – strings to parse

parse_to_string_list(words)

Parse field to string list.

Parameters:

words – strings to parse

print_interaction_parameters()

Print interaction parameters.

print_interaction_parameters_latex()

Print interaction parameters in LaTeX format.

print_interactions_latex()

Print interactions in LaTeX.